As a crucial antioxidant enzyme, glutathione peroxidase 3 (GPX3) has been found to be frequently repressed in many cancers due to promoter hypermethylation and is known as a possible tumor suppressor gene. In the present study, we investigated whether promoter hypermethylation of GPX3 and its repression are present in melanoma and, if so, whether GPX3 downregulation is implicated in the pathogenesis of melanoma. Our results revealed methylation of GPX3 and downregulation of its expression in both melanoma cell lines and surgical melanoma tissue samples. In melanoma cell lines, GPX3 expression was restored by treatment with 5-aza-2'-deoxycytidine both in mRNA and protein levels. Depletion of GPX3 was found to increase the proliferative ability, motility, and invasiveness of melanoma cells. Moreover, negative expression of GPX3 was related to poor prognosis in melanoma patients. These results suggest that methylation-mediated GPX3 repression may have critical implications for melanoma pathogenesis.